AtomLens Help Guide

Obscure Essentials™

Updated: March 14, 2026

Contents

Quick Start

1. Open your chemistry file with File > Open... or Command+O. You can select one file or several files at once.
2. If you prefer to start with search, use File > Browse... or Option+Command+O to open Molecule Browser and find files by filename, indexed chemistry keywords, reaction-only mode, or Finder label.
3. If you already copied structure text, choose File > New, paste it, then click Parse & Render or press Command+Return. This also works for pasted SMILES, CXSMILES, InChI, mol blocks, and reaction text.
4. Use the center canvas to inspect the drawing, then use the right sidebar to copy identifiers and review calculated properties.
5. If a source file contains many records, use File > Extract to split it into individual output files for easier downstream use.

What Is New in AtomLens 1.3

AtomLens 1.3 focuses on richer chemistry fidelity without making the app harder to use. The biggest user-visible additions are improved support for advanced text notations and a broader import and export surface that keeps more of the original chemical meaning intact.

• CXSMILES and Markush support: AtomLens can now open dedicated .cxsmiles files and depict supported CXSMILES layers such as Markush R-groups, repeat and link-node notation, and imported highlights.
• Fixed Markush legends: R-group member boxes stay below the main scaffold while the scaffold itself can still be rotated and inspected independently.
• Broader MDL and CML fidelity: V2000, V3000, SDF, and CML import and export behavior now preserves substantially more structure detail in supported molecule workflows.
• Reaction coverage expanded: AtomLens continues to support Reaction SMILES, RXN, and RDF, and now recognizes reaction content in CML as well.
• Highlight display choices: the highlight-style control lets you switch between no highlights, colored highlights, glow highlights, and glow highlights with a white edge.

Window Types

If a window is backed by a file, the title bar shows that file name and the macOS proxy icon. If you are working from pasted text only, the window title stays AtomLens until you save or export content.

User Interface Basics

Each document window is organized into three clear regions, so it is easy to understand where to type, where to inspect, and where to copy results:

• Left sidebar (Input): paste or type structure text, see format detection, clear input, and run parsing.
• Center panel (Canvas): interactive 2D drawing area for molecules or reactions. New documents are scaled to fit the visible canvas automatically so you start with a comfortable overview.
• Right sidebar (Overview): copy-ready identifiers and computed values for the current molecule selection.

Toolbar actions and quick controls are designed to keep common tasks one click away:

• Open: open one or more files into new document windows.
• Browse: jump to Molecule Browser for Spotlight-based lookup across your indexed files.
• Help: open this Help guide at any time without leaving your current workflow.
• Format detection chip: the Input panel shows the detected format, for example MDL Molfile, SMILES, or CXSMILES, so you can confirm what AtomLens recognized before or after parsing.
• Parse & Render: parses pasted text and updates the canvas and Overview sidebar in one step.
• Hide or Show Input Sidebar: Command+0.
• Hide or Show Overview Sidebar: Option+Command+0.

You can resize both sidebars by dragging the vertical divider lines, so you can prioritize the canvas or the text and details area as needed. In reaction documents, the participant table below the canvas is part of the same workflow and updates the Overview sidebar when you select a participant.

Canvas Interaction and Style Controls

The center canvas is where you inspect structures visually. Molecules and reactions use the same interaction model, so once you learn these controls, the experience stays consistent.

• Pan: click and drag in the canvas area to move around comfortably.
• Zoom: use the zoom slider, mouse wheel, or trackpad pinch to focus on fine details.
• Rotate: use the rotation slider or trackpad rotation gesture to change orientation.
• Reset: return to the default view at any time if you want to start fresh.
• Snapshot: copy a transparent PNG of the current drawing directly to the clipboard for reports or slides.
• Auto-fit first view: newly opened structures are scaled with padding so the whole depiction fits the available canvas before you begin to zoom or rotate.

Style toggles in the toolbar help you adapt the drawing to your current task and audience:

• Show Carbons: show or hide explicit carbon labels.
• Element Colors: color-code atoms by element type.
• Color Bonds: color bonds to match atom color mode when available.
• Aromatic Circles: switch aromatic ring visualization style.
• Highlight Style: choose how imported highlights should appear. This is especially useful for CXSMILES highlights and other annotated source formats.
• Map Colors: in reaction mode, highlight mapped atoms when map indices exist.
• Map Numbers: in reaction mode, show atom-map numbers when present.

Overview Sidebar

The Overview sidebar is your quick reference panel for the currently selected molecule context. It is especially useful when you need copy-ready identifiers, fast property checks, or quick confirmation before exporting.

• If a file has multiple molecules, use the picker at the top to move between entries.
• Common values include formula, mass values, heavy atom count, H-bond counts, ring count, and Rule of Five status.
• SMILES, ISO SMILES, InChI, and InChI Key include one-click copy buttons for quick reuse.
• In reaction mode, click a specific participant first to inspect that participant's details in the sidebar.
• For abstract or query-heavy structures such as some Markush inputs, generated identifiers like InChI may be unavailable. That is expected and reflects the abstract nature of the source.

Molecule Browser

Molecule Browser is the fastest way to navigate large local chemistry libraries. Instead of opening files one-by-one in Finder, you can search, sort, preview, and open results from one window. This is especially helpful when file names are inconsistent but metadata and structures are known. Browser cards combine a visual preview with chemistry metadata, path information, and Finder label state so you can decide what to open before leaving the results grid.

• Search: type text into the filter field and press Return or click Search to search by filename and indexed keywords such as SMILES, InChI, InChI Key, and other imported identifiers.
• Show only Reactions: turn on the reactions-only checkbox when you want the Browser to limit results to indexed reaction files.
• Finder label filters: click one or more Finder label dots in the filter bar to narrow the result set. If several labels are active, a file must match all of them to remain visible.
• Sort: sort by Modified Date, Creation Date, Molecular Weight, or LogP in ascending or descending order once metadata loading is complete.
• Selection: single-click for one file, Command-click for multi-select, Shift-click for ranges, or use the arrow keys to move through the grid from the keyboard.
• Open: double-click a card, press Return, or click Open Selected.
• Quick Look: press Space to open a floating preview inside AtomLens without opening the file into a document window.
• Finder label integration: the label buttons in the bottom toolbar let you add or remove Finder color labels on the selected files directly from AtomLens. Existing non-color Finder tags are preserved.
• Share and reveal: use the share button to send the selected files to standard macOS sharing destinations, or use Show in Finder when exactly one file is selected.

Result cards update as metadata arrives. Each card can show a thumbnail, formula, path, modified date, creation date, molecular weight, LogP, and Finder-label-aware background tint. If Spotlight has not indexed any supported chemistry files yet, AtomLens shows an info banner instead of an empty grid so you know why nothing appears.

Extract Tools

Extract tools are built for turning one source file into structured outputs. AtomLens first validates the source file, then asks where to save results, and then writes files or tables with clear progress feedback. This is useful for cleanup, QA, and handoff workflows where records either need to be split apart or summarized into a reviewable table.

Split multi-structure SDF into multiple files

1. Choose File > Extract > Split multi-structure SDF into multiple files....
2. Select an SDF file that contains two or more structures.
3. Confirm the detected structure count and choose a destination folder.
4. AtomLens writes one .sdf file per structure and shows progress while saving.

Extract multi-structure SDF attributes into a CSV table

1. Choose File > Extract > Extract multi-structure SDF attributes into CSV table....
2. Select a multi-structure SDF file.
3. Confirm the number of parsable structures and choose the destination .csv file.
4. AtomLens writes one CSV table that includes every annotated SDF field found across parsable records.

Every CSV cell is quoted. When a structure contains multiple values for the same field, AtomLens joins them with |. Invalid structures are skipped and the skipped count is reported at the end of the extraction.

Split multi-reaction SMILES into multiple files

1. Choose File > Extract > Split multi-reaction SMILES into multiple files....
2. Select a multi-line Reaction SMILES source file.
3. Confirm the number of valid reactions and choose a destination folder.
4. AtomLens writes one .rsmi file per valid reaction.

Split multi-reaction SMILES into multiple RXN files

1. Choose File > Extract > Split multi-reaction SMILES into multiple RXN files....
2. Select a multi-line Reaction SMILES source file.
3. Confirm the count, choose a destination folder, and start extraction.
4. AtomLens converts each valid reaction entry into an individual .rxn file.

If invalid Reaction SMILES lines are present, AtomLens skips them and includes the skipped count in the final status message. This helps you complete large extraction jobs while still seeing exactly what needs review.

Chemical Reaction Support

AtomLens supports reaction files directly, including .rsmi, .rxn, .rdf, and reaction-bearing .cml. You can open them from Finder, from File > Open..., or from Open Recent, just like molecule files.

• Reaction drawings include reactants, agents, products, plus signs, and reaction-arrow layout.
• The same pan, zoom, rotate, reset, and snapshot tools work in reaction mode.
• Reaction documents use a split layout: drawing on top, participant table below.
• The participant table is grouped by role with quick preview values.
• Selecting a participant updates the Overview sidebar so you can inspect that piece in detail.
• If atom-map numbers are available, Map Colors and Map Numbers are enabled automatically.

Reaction files are also supported in Quick Look previews and indexed into Spotlight metadata for local searching. This means you can still discover and preview reaction content quickly even before opening full documents.

CXSMILES, Markush, and Advanced Notation

AtomLens 1.3 adds end-user-visible support for modern CXSMILES features and related advanced annotations. You can open dedicated .cxsmiles files or paste SMILES text that contains a CX extension block such as |...|.

• Markush and R-groups: supported R-group definitions render as a main scaffold plus a clearly separated legend box underneath. This is useful for medicinal chemistry and patent-style structure families.
• Fixed legend behavior: rotating the main scaffold does not rotate the whole legend box. The legend stays under the main structure while each member fragment remains readable inside the box.
• Repeat and link-node notation: supported repeat-unit annotations and link-node ranges are drawn directly on the structure when present.
• Imported highlights: highlighted atoms and bonds from supported source formats can be shown with the Highlight Style control.
• Query and advanced annotations: AtomLens also depicts supported query atoms, query bonds, and Sgroup-style annotations that are commonly carried by modern MDL, CML, and CXSMILES sources.

Not every advanced source feature maps to every export format. In particular, File > Export... currently writes standard SMILES, not CXSMILES text, even if the imported source started as CXSMILES.

Supported Input Formats

AtomLens can open common molecule and reaction file types directly. If you are not sure what a format means, you can still open it and review the structure visually before deciding what to do next.

Important: .mol and .sdf input may use either V2000 or V3000 record syntax, and ordinary .smi or .smiles files may still contain CXSMILES extensions. AtomLens detects these automatically where possible.

Supported Export Formats

Use File > Export... to export the currently selected molecule context. The current Export command is molecule-focused; reaction documents remain view and inspection documents inside AtomLens. In most day-to-day workflows, SVG, SDF, and SMILES are the most common choices for sharing and downstream tooling.

Format Fidelity and Roundtrip Support

AtomLens 1.3 improves the fidelity of opening and writing supported chemistry formats. If you open a supported molecule file, inspect it, and export it again in a related supported molecule format, AtomLens now preserves far more of the imported chemistry detail than earlier versions.

• MDL V2000, V3000, and SDF: better preservation of coordinates, stereochemistry, Sgroups, highlights, query features, and related annotations supported by the chosen output format.
• CML: stronger read and write support for modern molecule CML and better recognition of reaction-bearing CML on import.
• CXSMILES: better parsing and depiction of advanced CX layers such as Markush R-groups, repeat and link-node annotations, highlights, and related structural metadata.
• Practical expectation: AtomLens aims to retain the important chemical meaning of the source format while still presenting a clear end-user workflow. Some source-specific constructs may still be visualized without having a one-click export target in the app.

Spotlight, Quick Look, and Finder Labels

AtomLens integrates with Finder so you can work faster without manually opening every file:

• Spotlight: AtomLens stores searchable chemistry metadata for local file lookup, including identifiers and reaction-aware summary text.
• Finder labels: Molecule Browser reads native Finder label and tag metadata from your files, uses it for filtering and card styling, and can update selected files when you change labels from the Browser toolbar.
• Quick Look in Finder: you get visual previews in Finder, including reaction files, before opening.
• Quick Look in Molecule Browser: pressing Space opens a larger floating preview window inside AtomLens for the current selection.
• Molecule Browser: combines Spotlight metadata, Quick Look thumbnails, and Finder label state to keep search and card browsing responsive.

Spotlight Metadata Fields

This section is mainly for advanced users and scripting workflows. AtomLens writes metadata keys prefixed with de_losko_atomlens_ so you can build precise local searches.

Molecule Browser also reads native macOS metadata such as kMDItemFSLabel and kMDItemUserTags so Finder color labels and tags remain visible and usable inside AtomLens.

Spotlight Search Examples

These Terminal examples are optional. You only need them if you want command-line filtering outside the app.

Find by exact InChI Key

mdfind 'de_losko_atomlens_inchi_key == "HVQAJTFOCKOKIN-UHFFFAOYSA-N"'

Find all AtomLens-indexed chemistry files

mdfind 'de_losko_atomlens_is_molecule == 1'

Find only reaction files

mdfind 'de_losko_atomlens_is_reaction == 1'

Find by molecular-weight range

mdfind 'de_losko_atomlens_molecular_weight >= 200 && de_losko_atomlens_molecular_weight <= 300'

Find Rule-of-Five compliant compounds

mdfind 'de_losko_atomlens_rule_of_five_compliant == 1'

Settings and Permissions

AtomLens keeps settings minimal on purpose. Most users only need to decide whether Molecule Browser should open automatically at launch. This keeps setup simple while still covering the most common preference.

• Open the Molecule Browser when launching AtomLens: enabled by default and useful if you usually start from search instead of opening a known file.
• Grant Access... (Home folder): optional permission helper for smoother reopen, search, Quick Look, and Finder-label update behavior in sandboxed macOS environments.

Troubleshooting

If something does not behave as expected, the checks below usually resolve it quickly. They cover the most common causes reported in everyday use.

• Parse button is disabled: your input is empty, or AtomLens cannot detect a supported structure format yet.
• Molecule Browser shows no files: Spotlight may still be indexing after AtomLens was installed, or there may not be any supported chemistry files in the searched locations yet.
• Molecule Browser label filters hide everything: active Finder label filters are combined, so a result must match every selected label.
• Extract workflow stops early: the selected source likely has only one valid record, and Extract requires multiple records.
• Map controls are disabled in reaction mode: the current reaction does not include atom-map numbers.
• InChI is unavailable for a Markush or query structure: abstract or query structures do not always have a direct InChI representation.
• Export is disabled while viewing a reaction: the current File > Export... workflow operates on molecule contexts rather than complete reaction documents.
• Finder labels do not update from Molecule Browser: open the file once through the file picker or grant access if macOS asks, then try the label action again.
• A file does not reopen from Search or Open Recent: open it once through the file picker and grant access if macOS asks.

Third-Party Software and Licenses

CDKSwiftNativePort repository: https://github.com/SaschaLosko/CDKSwiftNativePort

Privacy Notice

AtomLens is built for local-first desktop use. The points below summarize what that means in practice.

• AtomLens processes chemistry content locally on your Mac.
• No account or login is required for normal use.
• No cloud upload is required for parsing, viewing, browsing, exporting, or extraction workflows.
• Spotlight and Quick Look maintain local macOS indexes and preview caches.
• Finder label changes are written only to files you explicitly select in Molecule Browser.
• Export and extraction files are written only to destinations you explicitly choose.

Questions or bug reports: support@losko.de.

© 2026 Sascha Losko — Obscure Essentials™. All rights reserved.